Whole-Proteome Tree of Arthropods: An "alignment-free" phylogeny of proteome "books"

An "organism tree" of insects, the largest and most species-diverse group of all living animals, can be considered as a conceptual tree to capture a simplified narrative of the complex evolutionary courses of the extant insects. Currently, the most common approach has been to construct a "protein tree", as a surrogate for the organism tree, by Multiple Sequence Alignment (MSA) of highly homologous regions of a set of select proteins to represent each organism. However, such selected regions account for a very small fraction of the whole-proteome of each organism. Information Theory provides a method of comparing two sets of all proteins, two whole-proteomes, without MSA: By treating each whole-proteome sequence as a "book" of amino acid alphabets, the information contents of two whole-proteomes can be quantitatively compared using the text comparison method of the theory, without sequence alignment, providing an opportunity to construct a "whole-proteome tree" of insects as a surrogate for an organism tree of insects. A whole-proteome tree of the insects in this study shows that: (a) all the founders of the major groups of the insects have emerged in an explosive "burst" near the root of the tree, (b) the most basal group of all the insects is a subgroup of Hemiptera consisting of aphids and psyllids, and (c) there are other notable differences in the phylogeny of the groups compared to those of the recent protein trees of insects.